BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment

Descriptive analyses

Periods

Different time periods are specified for the analysis:

  • The data extraction period: Data extraction is foreseen from the first date of a documented SARS-CoV-2 infection in the population until the most recent date at which data is available at the time of analysis. All individuals vaccinated with at least one dose of the SARS-CoV-2 vaccine (any of the available brands) and all individuals eligible to be vaccinated with a documented positive diagnosis (irrespective of the type of test) for SARS-CoV-2 infection during the data extraction period are included in the study population.
  • The enrollment period: A sequence of nested (daily) trials are emulated with increasing time (t1, t2, …, tn), iterating over the days in the enrollment period. At each eligible time during the enrollment period, the vaccination status of eligible individuals is assessed and every individual who has completed a primary vaccination schedule at that time (coded here as initiation of the intervention strategy when emulating a nested target trial) is matched to an individual who has not (yet) completed the primary vaccination schedule (coded here as the control strategy when emulating a nested target trial).
  • The study period: The study period is considered from the start of the enrollment period until one year after the end of the enrollment period, to allow a minimal possible follow-up period of one year.
Period Time range
Data extraction period 2020-03-05 - 2022-05-19
Enrollment period 2021-01-01 - 2021-08-30
Study period 2021-01-01 - 2022-08-30

Study population and enrollment

A flow diagram displaying the process of obtaining a matched study population considered for survival analysis.

Description of the study population: table 1

Table 1
Completed a primary vaccination schedule during the enrollment period
(N=7757)		 Not completed a primary vaccination schedule during the enrollment period
(N=1126)		 P-value

ᵃ5-year age groups
sex_cd
0 136 (1.8%) 12 (1.1%) 0.0294
1 3663 (47.2%) 572 (50.8%)
2 3958 (51.0%) 542 (48.1%)
age_cdᵃ
10 905 (11.7%) 137 (12.2%) 0.73
11 1016 (13.1%) 133 (11.8%)
12 992 (12.8%) 158 (14.0%)
13 865 (11.2%) 112 (9.9%)
14 743 (9.6%) 107 (9.5%)
15 528 (6.8%) 83 (7.4%)
16 348 (4.5%) 49 (4.4%)
17 199 (2.6%) 25 (2.2%)
18 179 (2.3%) 27 (2.4%)
2 14 (0.2%) 1 (0.1%)
3 19 (0.2%) 0 (0%)
4 56 (0.7%) 7 (0.6%)
5 102 (1.3%) 13 (1.2%)
6 211 (2.7%) 24 (2.1%)
7 344 (4.4%) 49 (4.4%)
8 494 (6.4%) 83 (7.4%)
9 742 (9.6%) 118 (10.5%)
residence_area_cd
731 1211 (15.6%) 165 (14.7%) 0.708
732 1164 (15.0%) 171 (15.2%)
733 5382 (69.4%) 790 (70.2%)
pregnancy_bl
Yes 194 (2.5%) 42 (3.7%) 0.0216
No 7563 (97.5%) 1084 (96.3%)
institutionalized_bl
Yes 255 (3.3%) 20 (1.8%) 0.00917
No 6657 (85.8%) 974 (86.5%)
Missing 845 (10.9%) 132 (11.7%)
foreign_bl
Yes 1154 (14.9%) 153 (13.6%) 0.273
No 6603 (85.1%) 973 (86.4%)
socecon_lvl_cd
1 175 (2.3%) 23 (2.0%) 0.173
2 1069 (13.8%) 137 (12.2%)
3 2791 (36.0%) 425 (37.7%)
4 2682 (34.6%) 369 (32.8%)
5 1040 (13.4%) 172 (15.3%)
comorbidities_bl
Yes 3887 (50.1%) 549 (48.8%) 0.414
No 3870 (49.9%) 577 (51.2%)
immunestatus_bl
Yes 2154 (27.8%) 295 (26.2%) 0.287
No 5603 (72.2%) 831 (73.8%)
Table 1
Intervention group
(N=7757)		 Control group
(N=7757)		 P-value

ᵃ5-year age groups
sex_cd
0 136 (1.8%) 70 (0.9%) <0.001
1 3663 (47.2%) 3851 (49.6%)
2 3958 (51.0%) 3836 (49.5%)
age_cdᵃ
10 905 (11.7%) 1011 (13.0%) <0.001
11 1016 (13.1%) 1076 (13.9%)
12 992 (12.8%) 1056 (13.6%)
13 865 (11.2%) 873 (11.3%)
14 743 (9.6%) 745 (9.6%)
15 528 (6.8%) 517 (6.7%)
16 348 (4.5%) 324 (4.2%)
17 199 (2.6%) 153 (2.0%)
18 179 (2.3%) 150 (1.9%)
2 14 (0.2%) 4 (0.1%)
3 19 (0.2%) 10 (0.1%)
4 56 (0.7%) 34 (0.4%)
5 102 (1.3%) 72 (0.9%)
6 211 (2.7%) 165 (2.1%)
7 344 (4.4%) 316 (4.1%)
8 494 (6.4%) 499 (6.4%)
9 742 (9.6%) 752 (9.7%)
residence_area_cd
731 1211 (15.6%) 1153 (14.9%) 0.27
732 1164 (15.0%) 1132 (14.6%)
733 5382 (69.4%) 5472 (70.5%)
pregnancy_bl
Yes 194 (2.5%) 149 (1.9%) 0.0163
No 7563 (97.5%) 7608 (98.1%)
institutionalized_bl
Yes 292 (3.8%) 243 (3.1%) 0.0347
No 7465 (96.2%) 7514 (96.9%)
foreign_bl
Yes 1154 (14.9%) 1097 (14.1%) 0.202
No 6603 (85.1%) 6660 (85.9%)
socecon_lvl_cd
1 175 (2.3%) 82 (1.1%) <0.001
2 1069 (13.8%) 1037 (13.4%)
3 2791 (36.0%) 2921 (37.7%)
4 2682 (34.6%) 2762 (35.6%)
5 1040 (13.4%) 955 (12.3%)
comorbidities_bl
Yes 3887 (50.1%) 3891 (50.2%) 0.962
No 3870 (49.9%) 3866 (49.8%)
immunestatus_bl
Yes 2154 (27.8%) 2154 (27.8%) 1
No 5603 (72.2%) 5603 (72.2%)

Two-by-two tables

The individuals in the imported dataset are counted by whether they were fully vaccinated within the enrollment period and whether they experienced a known/confirmed infection (confirmed_case_bl, see CDM for definition).

Confirmed case No confirmed case Total
Completed a primary vaccination schedule during the enrollment period 2947 5801 8748
Didn’t complete a primary vaccination schedule during the enrollment period 394 858 1252
Total 3341 6659 10000

Ratio = \(\frac{(\frac{confirmed \ cases}{primary vaccinated \ individuals})} {(\frac{confirmed \ cases}{not-primary vaccinated \ individuals})}\) = 1.0704822

The individuals eligible for analysis are counted by whether they were fully vaccinated within the enrollment period and whether they experienced a known/confirmed infection (confirmed_case_bl, see CDM for definition).

Confirmed case No confirmed case Total
Completed a primary vaccination schedule during the enrollment period 2478 5279 7757
Didn’t complete a primary vaccination schedule during the enrollment period 330 796 1126
Total 2808 6075 8883

Ratio = \(\frac{(\frac{confirmed \ cases}{primary vaccinated \ individuals})} {(\frac{confirmed \ cases}{not-primary vaccinated \ individuals})}\) = 1.0900137

The matched individuals are counted by intervention group and whether they experienced a known/confirmed infection (confirmed_case_bl, see CDM for definition).

Confirmed case No confirmed case Total
Intervention group 2478 5279 7757
Control group 2039 5718 7757
Total 4517 10997 15514

Ratio = \(\frac{(\frac{confirmed \ cases}{primary vaccinated \ individuals})} {(\frac{confirmed \ cases}{not-primary vaccinated \ individuals})}\) = 1.2153016

Survival in un-matched population

Variable Beta (SE) HR (95% CI) P
fully_vaccinated_bl_bisTRUE 0.01 (0.07) 1.01 (0.88, 1.15) 0.93
Strata Time Number at risk Cumulative sum of number of events Cumulative sum of number censored Survival Std. error Cumulative hazard Std. error cumulative hazard
Fully vaccinated 0 1093 0 0 1.0000000 0.0000000000 0.0000000000 0.0000000000
Fully vaccinated 1 1093 0 0 1.0000000 0.0000000000 0.0000000000 0.0000000000
Fully vaccinated 100 1064 29 0 0.9734675 0.0048611561 0.0268748938 0.0049906903
Fully vaccinated 200 944 60 89 0.9447488 0.0069354617 0.0567982438 0.0073361433
Fully vaccinated 300 910 72 111 0.9324909 0.0076954581 0.0698496564 0.0082471116
Fully vaccinated 400 690 235 172 0.7568874 0.0138971237 0.2781052564 0.0183305791
Fully vaccinated 500 638 283 172 0.7039273 0.0148792711 0.3505367292 0.0211035233
Fully vaccinated 600 638 283 172 0.7039273 0.0148792711 0.3505367292 0.0211035233
Fully vaccinated 0 7757 283 172 1.0000000 0.0000000000 0.0000000000 0.0000000000
Fully vaccinated 1 7757 284 172 0.9998711 0.0001289075 0.0001289158 0.0001289158
Fully vaccinated 100 7653 388 172 0.9864638 0.0013120230 0.0136268117 0.0013298507
Fully vaccinated 200 3642 815 3833 0.9184806 0.0034924050 0.0849954454 0.0038004224
Fully vaccinated 300 2516 1266 4432 0.7799519 0.0067093405 0.2483253662 0.0085946669
Fully vaccinated 400 2232 1399 4593 0.7386179 0.0072482648 0.3027433080 0.0098052406
Fully vaccinated 500 756 1400 6073 0.7382516 0.0072539232 0.3032393397 0.0098177794
Fully vaccinated 600 2 1400 6810 0.7382516 0.0072539232 0.3032393397 0.0098177794
Variable Beta (SE) HR (95% CI) P
fully_vaccinated_bl_bisTRUE -0.03 (0.07) 0.97 (0.85, 1.12) 0.70
sex_cd
     1 (ref) – – –
     2 0.01 (0.06) 1.01 (0.90, 1.14) 0.80
     0 0.27 (0.20) 1.31 (0.89, 1.95) 0.18
age_cd
     2 (ref) – – –
     3 -1.37 (1.23) 0.25 (0.02, 2.81) 0.26
     4 -0.42 (0.78) 0.65 (0.14, 3.04) 0.59
     5 0.11 (0.74) 1.12 (0.26, 4.79) 0.88
     6 -0.17 (0.73) 0.85 (0.20, 3.54) 0.82
     7 -0.29 (0.72) 0.75 (0.18, 3.08) 0.69
     8 -0.12 (0.72) 0.89 (0.22, 3.61) 0.87
     9 -0.32 (0.71) 0.72 (0.18, 2.93) 0.65
     10 -0.20 (0.71) 0.82 (0.20, 3.29) 0.77
     11 -0.15 (0.71) 0.86 (0.21, 3.48) 0.84
     12 -0.38 (0.71) 0.69 (0.17, 2.77) 0.60
     13 -0.24 (0.71) 0.78 (0.19, 3.17) 0.73
     14 -0.27 (0.71) 0.76 (0.19, 3.09) 0.70
     15 -0.21 (0.72) 0.81 (0.20, 3.28) 0.76
     16 -0.27 (0.72) 0.76 (0.19, 3.14) 0.71
     17 -0.22 (0.73) 0.80 (0.19, 3.36) 0.76
     18 -0.41 (0.74) 0.66 (0.16, 2.80) 0.58
residence_area_cd
     731 (ref) – – –
     732 -0.11 (0.10) 0.90 (0.73, 1.10) 0.31
     733 -0.05 (0.08) 0.95 (0.81, 1.11) 0.52
pregnancy_blTRUE 0.10 (0.17) 1.10 (0.79, 1.52) 0.57
institutionalized_blTRUE 0.01 (0.16) 1.01 (0.74, 1.38) 0.95
foreign_blTRUE -0.02 (0.08) 0.98 (0.84, 1.15) 0.84
socecon_lvl_cd
     1 (ref) – – –
     2 -0.04 (0.21) 0.96 (0.64, 1.44) 0.85
     3 -0.09 (0.20) 0.91 (0.62, 1.35) 0.65
     4 -0.07 (0.20) 0.94 (0.63, 1.38) 0.74
     5 -0.01 (0.21) 0.99 (0.66, 1.49) 0.98
comorbidities_blTRUE 0.03 (0.06) 1.03 (0.93, 1.16) 0.55
immunestatus_blTRUE -0.06 (0.06) 0.94 (0.83, 1.07) 0.35